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Folding Funnel
The folding funnel hypothesis is a specific version of the energy landscape theory of protein folding, which assumes that a protein's native state corresponds to its free energy minimum under the solution conditions usually encountered in cells. Although energy landscapes may be "rough", with many non-native local minima in which partially folded proteins can become trapped, the folding funnel hypothesis assumes that the native state is a deep free energy minimum with steep walls, corresponding to a single well-defined tertiary structure. The term was introduced by Ken A. Dill in a 1987 article discussing the stabilities of globular proteins. The folding funnel hypothesis is closely related to the hydrophobic collapse hypothesis, under which the driving force for protein folding is the stabilization associated with the sequestration of hydrophobic amino acid side chains in the interior of the folded protein. This allows the water solvent to maximize its entropy, lowering the tot ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Folding Funnel Schematic
Fold, folding or foldable may refer to: Arts, entertainment, and media * ''Fold'' (album), the debut release by Australian rock band Epicure *Fold (poker), in the game of poker, to discard one's hand and forfeit interest in the current pot *Above the fold and below the fold, the positioning of news items on a newspaper's front page according to perceived importance *Paper folding, or ''origami'', the art of folding paper Science, technology, and mathematics Biology *Protein folding, the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure **Folding@home, a powerful distributed-computing project for simulating protein folding *Fold coverage, quality of a DNA sequence *Skin fold, an area of skin that folds Computing *Fold (higher-order function), a type of programming operation on data structures *fold (Unix), a computer program used to wrap lines to fit in a specified width *Folding (DSP implementation), a transformation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Native Contact
In protein folding, a native contact is a contact between the side chains of two amino acids that are not neighboring in the amino acid sequence (i.e., they are more than four residues apart in the primary sequence in order to remove trivial i to i+4 contacts along alpha helices) but are spatially close in the protein's native state tertiary structure. The fraction of native contacts reproduced in a particular structure is often used as a reaction coordinate for measuring the deviation from the native state of structures produced during molecular dynamics simulations or in benchmarks of protein structure prediction methods. The contact order is a measure of the locality of a protein's native contacts; that is, the sequence distance between amino acids that form contacts. Proteins with low contact order are thought to fold faster and some may be candidates for downhill folding Downhill folding is a process in which a protein folds without encountering any significant macroscopic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amino Acid Sequence
Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequences. Formation Biological Amino acids are polymerised via peptide bonds to form a long backbone, with the different amino acid side chains protruding along it. In biological systems, proteins are produced during translation by a cell's ribosomes. Some organisms can also make short peptides by non-ribosomal peptide synthesis, which often use amino acids other than the standard 20, and may be cyclised, modified and cross-linked. Chemical Peptides can be synthesised chemically via a range of laboratory methods. Chemical methods typically synthe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
The Blind Watchmaker
''The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design'' is a 1986 book by Richard Dawkins, in which the author presents an explanation of, and argument for, the theory of evolution by means of natural selection. He also presents arguments to refute certain criticisms made on his first book, ''The Selfish Gene''. (Both books espouse the gene-centric view of evolution.) An unabridged audiobook edition was released in 2011, narrated by Richard Dawkins and Lalla Ward. Overview In his choice of the title for this book, Dawkins refers to the watchmaker analogy made famous by William Paley in his 1802 book ''Natural Theology''. Paley, writing long before Charles Darwin published ''On the Origin of Species'' in 1859, held that the complexity of living organisms was evidence of the existence of a divine creator by drawing a parallel with the way in which the existence of a watch compels belief in an intelligent watchmaker. Dawkins, in contrasting t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
The Blind Watchmaker
''The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design'' is a 1986 book by Richard Dawkins, in which the author presents an explanation of, and argument for, the theory of evolution by means of natural selection. He also presents arguments to refute certain criticisms made on his first book, ''The Selfish Gene''. (Both books espouse the gene-centric view of evolution.) An unabridged audiobook edition was released in 2011, narrated by Richard Dawkins and Lalla Ward. Overview In his choice of the title for this book, Dawkins refers to the watchmaker analogy made famous by William Paley in his 1802 book ''Natural Theology''. Paley, writing long before Charles Darwin published ''On the Origin of Species'' in 1859, held that the complexity of living organisms was evidence of the existence of a divine creator by drawing a parallel with the way in which the existence of a watch compels belief in an intelligent watchmaker. Dawkins, in contrasting t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gibbs Free Energy
In thermodynamics, the Gibbs free energy (or Gibbs energy; symbol G) is a thermodynamic potential that can be used to calculate the maximum amount of work that may be performed by a thermodynamically closed system at constant temperature and pressure. It also provides a necessary condition for processes such as chemical reactions that may occur under these conditions. The Gibbs free energy change , measured in joules in SI) is the ''maximum'' amount of non-expansion work that can be extracted from a closed system (one that can exchange heat and work with its surroundings, but not matter) at fixed temperature and pressure. This maximum can be attained only in a completely reversible process. When a system transforms reversibly from an initial state to a final state under these conditions, the decrease in Gibbs free energy equals the work done by the system to its surroundings, minus the work of the pressure forces. The Gibbs energy is the thermodynamic potential that is minim ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Energy Landscape
An energy landscape is a mapping of possible states of a system. The concept is frequently used in physics, chemistry, and biochemistry, e.g. to describe all possible conformations of a molecular entity, or the spatial positions of interacting molecules in a system, or parameters and their corresponding energy levels, typically Gibbs free energy. Geometrically, the energy landscape is the graph of the energy function across the configuration space of the system. The term is also used more generally in geometric perspectives to mathematical optimization, when the domain of the loss function is the parameter space of some system. Applications The term is useful when examining protein folding; while a protein can theoretically exist in a nearly infinite number of conformations along its energy landscape, in reality proteins fold (or "relax") into secondary and tertiary structures that possess the lowest possible free energy. The key concept in the energy landscape approach to pro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chaperone (protein)
In molecular biology, molecular chaperones are proteins that assist the conformational folding or unfolding of large proteins or macromolecular protein complexes. There are a number of classes of molecular chaperones, all of which function to assist large proteins in proper protein folding during or after synthesis, and after partial denaturation. Chaperones are also involved in the translocation of proteins for proteolysis. The first molecular chaperones discovered were a type of assembly chaperones which assist in the assembly of nucleosomes from folded histones and DNA. One major function of molecular chaperones is to prevent the aggregation of misfolded proteins, thus many chaperone proteins are classified as heat shock proteins, as the tendency for protein aggregation is increased by heat stress. The majority of molecular chaperones do not convey any steric information for protein folding, and instead assist in protein folding by binding to and stabilizing folding interme ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Levinthal's Paradox
Levinthal's paradox is a thought experiment, also constituting a self-reference in the theory of protein folding. In 1969, Cyrus Levinthal noted that, because of the very large number of degrees of freedom in an unfolded polypeptide chain, the molecule has an astronomical number of possible conformations. An estimate of 10300 was made in one of his papers (often incorrectly cited as the 1968 paper). For example, a polypeptide of 100 residues will have 99 peptide bonds, and therefore 198 different phi and psi bond angles. If each of these bond angles can be in one of three stable conformations, the protein may misfold into a maximum of 3198 different conformations (including any possible folding redundancy). Therefore, if a protein were to attain its correctly folded configuration by sequentially sampling all the possible conformations, it would require a time longer than the age of the universe to arrive at its correct native conformation. This is true even if conformations are ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Native Structure
Native may refer to: People * Jus soli, citizenship by right of birth * Indigenous peoples, peoples with a set of specific rights based on their historical ties to a particular territory ** Native Americans (other) In arts and entertainment * Native (band), a French R&B band * Native (comics), a character in the X-Men comics universe * ''Native'' (album), a 2013 album by OneRepublic * ''Native'' (2016 film), a British science fiction film * ''The Native'', a Nigerian music magazine In science * Native (computing), software or data formats supported by a certain system * Native language, the language(s) a person has learned from birth * Native metal, any metal that is found in its metallic form, either pure or as an alloy, in nature * Native species, a species whose presence in a region is the result of only natural processes Other uses * Northeast Arizona Technological Institute of Vocational Education (NATIVE), a technology school district in the Arizona portion of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Justin L
Justin may refer to: People * Justin (name), including a list of persons with the given name Justin * Justin (historian), a Latin historian who lived under the Roman Empire * Justin I (c. 450–527), or ''Flavius Iustinius Augustus'', Eastern Roman Emperor who ruled from 518 to 527 * Justin II (c. 520–578), or ''Flavius Iustinius Iunior Augustus'', Eastern Roman emperor who ruled from 565 to 578 * Justin (magister militum per Illyricum) (''fl.'' 538–552), a Byzantine general * Justin (Moesia), a Byzantine general killed in battle in 528 * Justin (consul 540) (c. 525–566), a Byzantine general * Justin Martyr (103–165), a Christian martyr * Justin (gnostic), 2nd-century Gnostic Christian; sometimes confused with Justin Martyr * Justin the Confessor (d 269) * Justin of Chieti, venerated as an early bishop of Chieti, Italy * Justin of Siponto (c. 4th century), venerated as Christian martyrs by the Catholic Church * Justin de Jacobis (1800–1860), an Italian Lazarist missionar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Funnel
A funnel is a tube or pipe that is wide at the top and narrow at the bottom, used for guiding liquid or powder into a small opening. Funnels are usually made of stainless steel, aluminium, glass, or plastic. The material used in its construction should be sturdy enough to withstand the weight of the substance being transferred, and it should not react with the substance. For this reason, stainless steel or glass are useful in transferring diesel, while plastic funnels are useful in the kitchen. Sometimes disposable paper funnels are used in cases where it would be difficult to adequately clean the funnel afterwards (for example, in adding motor oil into a car). Dropper funnels, also called dropping funnels or tap funnels, have a tap to allow the controlled release of a liquid. A flat funnel, made of polypropylene, utilises living hinges and flexible walls to fold flat. The term "funnel" may refer to the chimney or smokestack on a steam locomotive and commonly refers to the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
